LAMMPS (18 Jul 2015)
# 250 butane system for drude polarizability example (Nose-Hoover)

units real
boundary p p p

atom_style full
bond_style harmonic
angle_style harmonic
dihedral_style opls
special_bonds lj/coul 0.0 0.0 0.5

pair_style hybrid/overlay lj/cut/coul/long 8.0 8.0 thole 2.089 8.0
pair_modify mix geometric tail yes
kspace_style pppm 1.0e-4

read_data data.butane
  orthogonal box = (-19.1 -19.0999 -19.1) to (19.1 19.1 19.1)
  2 by 1 by 2 MPI processor grid
  reading atoms ...
  4500 atoms
  scanning bonds ...
  5 = max bonds/atom
  scanning angles ...
  6 = max angles/atom
  scanning dihedrals ...
  9 = max dihedrals/atom
  reading bonds ...
  4250 bonds
  reading angles ...
  6000 angles
  reading dihedrals ...
  6750 dihedrals
  5 = max # of 1-2 neighbors
  8 = max # of 1-3 neighbors
  12 = max # of 1-4 neighbors
  17 = max # of special neighbors

group gBUTANE molecule 1:250
4500 atoms in group gBUTANE
group gCORES type 1 2 3
3500 atoms in group gCORES
group gDRUDES type 4 5
1000 atoms in group gDRUDES

pair_coeff    1    1 lj/cut/coul/long 0.065997 3.500000 # C3H C3H
pair_coeff    1    2 lj/cut/coul/long 0.065997 3.500000 # C3H C2H
pair_coeff    1    3 lj/cut/coul/long 0.044496 2.958040 # C3H H
pair_coeff    2    2 lj/cut/coul/long 0.065997 3.500000 # C2H C2H
pair_coeff    2    3 lj/cut/coul/long 0.044496 2.958040 # C2H H
pair_coeff    3    3 lj/cut/coul/long 0.029999 2.500000 # H H
pair_coeff    *  4*5 lj/cut/coul/long 0.000000 0.000000 # No lj for drudes
pair_coeff    1    * thole 1.368000
pair_coeff    2    * thole 1.368000
pair_coeff    4    * thole 1.368000
pair_coeff    5    * thole 1.368000

neighbor 2.0 bin

variable vTEMP   equal 260.0
variable vTEMP_D equal 1.0
variable vPRESS  equal 1.0

velocity gCORES  create ${vTEMP} 12345
velocity gCORES  create 260 12345
velocity gDRUDES create ${vTEMP_D} 12345
velocity gDRUDES create 1 12345

fix fDRUDE all drude C C N D D

fix fSHAKE gCORES shake 0.0001 20 0 b 2 4
  0 = # of size 2 clusters
  500 = # of size 3 clusters
  500 = # of size 4 clusters
  0 = # of frozen angles

comm_modify vel yes
compute cTEMP_CORE gCORES temp/com
compute cTEMP all temp/drude

fix fDIRECT all drude/transform/direct
fix fNVT1 gCORES nvt temp ${vTEMP} ${vTEMP} 100.0
fix fNVT1 gCORES nvt temp 260 ${vTEMP} 100.0
fix fNVT1 gCORES nvt temp 260 260 100.0
fix fNVT2 gDRUDES nvt temp ${vTEMP_D} ${vTEMP_D} 20.0
fix fNVT2 gDRUDES nvt temp 1 ${vTEMP_D} 20.0
fix fNVT2 gDRUDES nvt temp 1 1 20.0
fix fINVERSE all drude/transform/inverse

fix fMOMENTUM all momentum 100 linear 1 1 1

thermo_style custom step cpu etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2]
thermo 50

timestep 0.5
run 2000
PPPM initialization ...
  G vector (1/distance) = 0.367867
  grid = 36 36 36
  stencil order = 5
  estimated absolute RMS force accuracy = 0.031354
  estimated relative force accuracy = 9.44215e-05
  using double precision FFTs
  3d grid and FFT values/proc = 26875 11664
Rebuild special list taking Drude particles into account
Old max number of 1-2 to 1-4 neighbors: 17
New max number of 1-2 to 1-4 neighbors: 17 (+0)
Neighbor list info ...
  2 neighbor list requests
  update every 1 steps, delay 10 steps, check yes
  master list distance cutoff = 10
  ghost atom cutoff = 10
Memory usage per processor = 14.7792 Mbytes
Step CPU TotEng KinEng Temp PotEng E_bond E_angle E_dihed E_impro E_vdwl E_coul E_long Press Volume cTEMP[1] cTEMP[2] 
       0            0    6535.5187      2714.74    248.45112    3820.7787    3724.3278    140.75328    1.4735401            0   -518.77975    595169.42   -594696.41    -353319.1    55742.797    334.61375    18.435655 
      50     1.019057    2130.0808    1490.8248    136.43926    639.25599    192.16834    670.26518    115.15685            0    -766.5636    595300.83    -594872.6    2829.5958    55742.797    187.32686   0.60253137 
     100     2.043848    2172.0553    1656.5476    151.60609    515.50769    180.41449    708.03397    165.80788            0   -971.62525    595305.35   -594872.47     1231.388    55742.797    208.34096   0.16151117 
     150    3.0405529     2216.471    1733.4485      158.644    483.02256    136.16281    713.34485    169.62608            0   -964.30363    595300.47   -594872.27    4400.6233    55742.797    218.02975   0.12336381 
     200    4.0440719    2271.1314    1750.9955     160.2499    520.13584    190.12953    725.63606    167.04635            0   -987.11203     595295.5   -594871.06     2107.495    55742.797    220.19714   0.23035002 
     250    5.0482569    2333.7821    1793.0252    164.09642    540.75694    153.18169    833.95288     168.1507            0   -1041.2955     595297.2   -594870.43    1165.6922    55742.797    225.18334    1.0339003 
     300     6.044857    2403.6147    1909.3441    174.74185    494.27053      144.273     803.8452    155.85505            0   -1036.4615    595297.31   -594870.55    2511.3723    55742.797    239.06243    3.0455683 
     350    7.0382209     2448.239      1862.67    170.47027    585.56896    181.70522    821.79171    164.10713            0   -1005.4167     595293.5   -594870.12    2874.0826    55742.797    233.92745    1.0806438 
     400     8.025661    2498.6992    1942.5496    177.78079    556.14963     168.5792    828.99116     182.0756            0    -1050.149    595296.43   -594869.77    485.86784    55742.797    244.23632   0.38827289 
     450     9.010309    2552.9639    1890.0917    172.97988    662.87225    134.42613     957.3361    181.42951            0   -1036.4237    595295.53   -594869.43    66.452466    55742.797    237.65323   0.34464586 
     500     9.979717    2608.5501    1970.0729    180.29971    638.47718    187.01392    838.62128    176.10774            0   -985.23355    595290.89   -594868.93    3471.1636    55742.797    247.59402   0.66791289 
     550    10.965174     2667.002    1875.8227      171.674    791.17932    178.48766    1003.6885    176.78987            0   -991.21707    595292.35   -594868.92    1767.0547    55742.797    235.34039    1.7252612 
     600    11.944224    2715.2397     1883.279    172.35639    831.96067    186.79504    1047.6877     183.0431            0   -1010.5423    595293.27   -594868.29    931.85415    55742.797    236.28437    1.7094243 
     650    12.916431    2754.4495     1970.794    180.36571    783.65547    166.02823    963.09393    184.84638            0   -952.45216    595290.25   -594868.11    2640.0169    55742.797    247.67755   0.68709272 
     700    13.889729    2795.9463    1928.2674    176.47369    867.67893    176.09642    1002.4636    186.11482            0   -920.14357    595291.32   -594868.18    664.78857    55742.797    242.41896   0.44316458 
     750    14.849284    2838.2051    2043.2257     186.9946    794.97938    170.34989    941.73149    193.53082            0   -940.49605     595298.1   -594868.23    410.24692    55742.797    256.84034   0.55228895 
     800    15.765569    2881.9786    1945.9721    178.09402    936.00653    197.52035    1021.5571    202.83523            0   -915.18508    595297.49   -594868.21    -716.8133    55742.797    244.35111    1.2303486 
     850     16.62147     2923.386    2106.5752    192.79231    816.81079     195.9499     886.4168    184.36063            0   -878.10486    595296.29    -594868.1   -1407.5716    55742.797     264.3276    1.8387295 
     900    17.476931    2950.6672    2039.6221     186.6648    911.04508     183.7962    1000.7955    184.49765            0   -890.38971    595299.97   -594867.63    -1085.795    55742.797    256.21167    1.0198179 
     950    18.332394    2976.6435    2006.5931    183.64202    970.05037    228.60059    985.21322    206.18531            0   -881.65816    595299.54   -594867.83   -1851.9704    55742.797    252.23636   0.54012295 
    1000    19.192022    3003.7432    2056.8471    188.24122    946.89612    171.73291    976.85679    207.05089            0   -836.24565    595294.95   -594867.45    282.61893    55742.797     258.5658   0.52076763 
    1050    20.070536    3031.3535    2095.4845    191.77729    935.86893    203.54188    945.75571    204.85039            0   -846.10968    595294.45   -594866.62   -376.91144    55742.797    263.27092   0.93584075 
    1100    20.978902    3058.5346    2047.3099    187.36839    1011.2247    211.94079     1001.093    223.66207            0   -855.82432    595297.13   -594866.78   -1381.6546    55742.797    256.93411    1.6724371 
    1150    21.886788    3078.3992    2123.1811    194.31206    955.21814    189.50191    937.18689    224.21463            0   -823.63239    595294.38   -594866.43    524.69914    55742.797    266.59741    1.3568273 
    1200    22.731807    3093.5558    2005.8937    183.57801    1087.6621    201.34278     1044.991    219.39206            0   -805.37129    595293.83   -594866.52   -370.32731    55742.797    252.08289   0.71475598 
    1250    23.577332    3108.5154    2175.8971     199.1366    932.61825    156.65715    969.72264    225.30585            0   -850.00508    595297.25   -594866.31   -1015.3099    55742.797    273.53152   0.55101046 
    1300     24.41954     3122.979    2090.3725    191.30944    1032.6065    209.92008    984.36627    236.75348            0   -825.27575    595292.92   -594866.08   -798.51517    55742.797    262.69428   0.75855174 
    1350    25.260247    3136.8213    2084.4701    190.76926    1052.3512    186.49846    1004.7564    234.55382            0   -798.08358    595290.25   -594865.63    702.53502    55742.797    261.71554    1.3884097 
    1400    26.111855    3144.9027    2180.3656    199.54555    964.53705    170.02479    962.43949    235.07796            0    -829.2718    595291.77   -594865.51    1682.2458    55742.797    273.72857    1.5246347 
    1450    26.950639    3146.3362    2013.3813    184.26326     1132.955    193.77936    1084.1402    252.32287            0   -821.23025    595288.54    -594864.6   -160.21134    55742.797    252.96371   0.87779957 
    1500    27.790502    3150.6919    2107.4861    192.87567    1043.2058    185.11758    988.72513    245.47693            0   -796.86696    595285.47   -594864.71    2242.3607    55742.797    264.90213   0.61222945 
    1550    28.619789    3156.3482    2074.5978    189.86575    1081.7504    166.52858    1062.4966    238.93331            0   -810.65249    595289.34    -594864.9    2224.9023    55742.797     260.7359   0.68881915 
    1600    29.460929    3163.8714    2000.6737    183.10027    1163.1978    210.70797    1110.4522    256.16659            0   -840.14623    595290.73   -594864.71   -830.17835    55742.797    251.26509    1.1443132 
    1650    30.299437    3169.3484    2056.4317    188.20321    1112.9167    214.64223    1021.7623    268.00145            0    -815.6963       595289    -594864.8    813.10459    55742.797    258.12846    1.5476742 
    1700    31.139599    3168.7665    2119.4084    193.96679    1049.3581    147.25025    1027.6419    246.49323            0   -797.55219    595290.74   -594865.22    412.56019    55742.797    266.23023    1.0703144 
    1750    31.982883    3168.2311    2066.7649    189.14889    1101.4662    224.43981    1005.0038    243.56888            0   -797.82899    595291.25   -594864.96    -858.8853    55742.797    259.74652   0.69941609 
    1800    32.826623    3169.7582    2109.6043    193.06952     1060.154    204.57671    981.05578    249.38028            0   -801.42264    595291.51   -594864.95    137.07377    55742.797     265.1523   0.65571522 
    1850    33.670608    3174.8602    2133.4946    195.25594    1041.3657    175.87741    982.18471    244.56078            0   -786.49062    595290.44   -594865.21    882.07943    55742.797    268.02634    1.0063027 
    1900    34.515605     3180.392     2106.493    192.78478    1073.8991    207.88481    977.47602    250.68433            0   -788.04013    595290.55   -594864.66    574.47687    55742.797    264.45328    1.4759962 
    1950    35.361549    3182.9198    2084.8984    190.80846    1098.0214    207.26715    1007.5534    256.52264            0   -800.37486    595291.76   -594864.71   -981.72234    55742.797    261.81317    1.2717649 
    2000    36.208456     3185.292    2079.8093    190.34271    1105.4827    185.44479    1008.7001    251.06381            0   -766.97114    595292.22   -594864.97    661.65731    55742.797     261.3551   0.78598984 
Loop time of 36.2086 on 4 procs for 2000 steps with 4500 atoms

Pair  time (%) = 15.6569 (43.2408)
Bond  time (%) = 4.33273 (11.966)
Kspce time (%) = 10.271 (28.3662)
Neigh time (%) = 0.435532 (1.20284)
Comm  time (%) = 0.83936 (2.31813)
Outpt time (%) = 0.00456434 (0.0126057)
Other time (%) = 4.66849 (12.8933)

Nlocal:    1125 ave 1165 max 1096 min
Histogram: 2 0 0 0 0 0 1 0 0 1
Nghost:    5854.5 ave 5931 max 5788 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Neighs:    193727 ave 200966 max 187020 min
Histogram: 2 0 0 0 0 0 0 0 0 2

Total # of neighbors = 774908
Ave neighs/atom = 172.202
Ave special neighs/atom = 13.3333
Neighbor list builds = 35
Dangerous builds = 0
